genome

Convert Genome Assembly Data Report into TSV format

genome

Convert Genome Assembly Data Report into TSV format

Name

dataformat tsv genome - Convert Genome Assembly Data Report into TSV format

Synopsis

dataformat tsv genome [flags]

Description

Convert Genome Assembly Data Report into TSV format.

Refer to NCBI’s command line start documentation for information about getting started with the command-line tools.

Examples

  dataformat tsv genome --inputfile human/ncbi_dataset/data/assembly_data_report.jsonl
  dataformat tsv genome --package human.zip

Options

      --elide-header       Do not output header
      --fields strings     comma-separated list of fields
  -h, --help               help for genome
      --inputfile string   input file
      --package string     datasets package (zip archive), inputfile parameter is relative to the root path inside the archive

Fields

MnemonicName
annotinfo-busco-completeAnnotation Info BUSCO Complete
annotinfo-busco-duplicatedAnnotation Info BUSCO Duplicated
annotinfo-busco-fragmentedAnnotation Info BUSCO Fragmented
annotinfo-busco-lineageAnnotation Info BUSCO Lineage
annotinfo-busco-missingAnnotation Info BUSCO Missing
annotinfo-busco-singlecopyAnnotation Info BUSCO Single Copy
annotinfo-busco-totalcountAnnotation Info BUSCO Total Count
annotinfo-busco-verAnnotation Info BUSCO Version
annotinfo-featcount-gene-non-codingAnnotation Info Count Gene Non-coding
annotinfo-featcount-gene-otherAnnotation Info Count Gene Other
annotinfo-featcount-gene-protein-codingAnnotation Info Count Gene Protein-coding
annotinfo-featcount-gene-pseudogeneAnnotation Info Count Gene Pseudogene
annotinfo-featcount-gene-totalAnnotation Info Count Gene Total
annotinfo-nameAnnotation Info Name
annotinfo-release-dateAnnotation Info Release Date
annotinfo-report-urlAnnotation Info Report URL
annotinfo-sourceAnnotation Info Source
assminfo-accessionAssembly Accession
assminfo-bioproject-lineage-accessionAssembly BioProject Lineage Accession
assminfo-bioproject-lineage-parent-accessionsAssembly BioProject Lineage Parent Accessions
assminfo-bioproject-lineage-titleAssembly BioProject Lineage Title
assminfo-biosample-accessionAssembly BioSample Accession
assminfo-blast-urlAssembly Blast URL
assminfo-descriptionAssembly Description
assminfo-genbank-assm-accessionAssembly GenBank Accession
assminfo-levelAssembly Level
assminfo-linked-assmAssembly Linked Assembly
assminfo-nameAssembly Name
assminfo-paired_accessionAssembly Paired Accession
assminfo-refseq-assm-accessionAssembly RefSeq Accession
assminfo-refseq-categoryAssembly Refseq Dategory
assminfo-sequencing-techAssembly Sequencing Tech
assminfo-submission-dateAssembly Submission Date
assminfo-submitterAssembly Submitter
assminfo-typeAssembly Type
assminfo-ucsc-assm-nameAssembly UCSC Assembly Name
assmstats-contig-l50Assembly Stats Contig L50
assmstats-contig-n50Assembly Stats Contig N50
assmstats-gaps-between-scaffolds-countAssembly Stats Gaps Between Scaffolds Count
assmstats-gc-countAssembly Stats GC Count
assmstats-number-of-component-sequencesAssembly Stats Number of Component Sequences
assmstats-number-of-contigsAssembly Stats Number of Contigs
assmstats-number-of-scaffoldsAssembly Stats Number of Scaffolds
assmstats-scaffold-l50Assembly Stats Scaffold L50
assmstats-scaffold-n50Assembly Stats Scaffold N50
assmstats-total-number-of-chromosomesAssembly Stats Total Number of Chromosomes
assmstats-total-sequence-lenAssembly Stats Total Sequence Length
assmstats-total-ungapped-lenAssembly Stats Total Ungapped Length
breedBreed
common-nameCommon name
cultivarCultivar
ecotypeEcotype
isolateIsolate
organelle-assembly-nameOrganelle Assembly Name
organelle-bioproject-accessionsOrganelle BioProject Accessions
organelle-descriptionOrganelle Description
organelle-infraspecific-nameOrganelle Infraspecific Name
organelle-submitterOrganelle Submitter
organelle-total-seq-lengthOrganelle Total Seq Length
organism-nameOrganism name
sexSex
strainStrain
tax-idTaxonomic ID
wgs-contigs-urlWGS contigs URL
wgs-project-accessionWGS project accession
wgs-urlWGS URL
Generated October 22, 2021